P16 methylation increases the sensitivity of cancer cells to the CDK4/6 inhibitor palbociclib.

Paiyun Li,Dajun Deng,Xuehong Zhang,Liankun Gu,Jing Zhou,Yuan-Jia Chen

doi:10.1371/journal.pone.0223084

Abstract

The P16 (CDKN2Aink4a) gene is an endogenous CDK4/6 inhibitor. Palbociclib (PD0332991) is an anti-CDK4/6 chemical for cancer treatment. P16 is most frequently inactivated by copy number deletion and DNA methylation in cancers. It is well known that cancer cells with P16 deletion are more sensitive to palbociclib than those without. However, whether P16 methylation is related to palbociclib sensitivity is not known. By analyzing public pharmacogenomic datasets, we found that the IC50 of palbociclib in cancer cell lines (n = 522) was positively correlated with both the P16 expression level and P16 gene copy number. Our experimental results further showed that cancer cell lines with P16 methylation were more sensitive to palbociclib than those without. To determine whether P16 methylation directly increased the sensitivity of cancer cells to palbociclib, we induced P16 methylation in the lung cancer cell lines H661 and HCC827 and the gastric cancer cell line BGC823 via an engineered P16-specific DNA methyltransferase (P16-Dnmt) and found that the sensitivity of these cells to palbociclib was significantly increased. The survival rate of P16-Dnmt cells was significantly lower than that of vector control cells 48 hrs post treatment with palbociclib (10 μM). Notably, palbociclib treatment also selectively inhibited the proliferation of the P16-methylated subpopulation of P16-Dnmt cells, further indicating that P16 methylation can increase the sensitivity of cells to this CDK4/6 inhibitor. These results were confirmed in an animal experiment. In conclusion, inactivation of the P16 gene by DNA methylation can increase the sensitivity of cancer cells to palbociclib.

Highlights

The ability to sustain uncontrolled cell proliferation is one of the hallmarks of cancer cells [1]
We systematically investigated the relationship between P16 methylation and the sensitivity of cancer cells to the CDK4/6 inhibitor palbociclib using both public datasets and cell models of P16 methylation induced by an artificial P16-specific methyltransferase (P16-Dnmt) [29]
To explore the relationship between P16 methylation and the sensitivity of cancer cells to palbociclib, we first analyzed the correlation between the half-maximal inhibitory concentration (IC50) levels of palbociclib in 522 cell lines and the transcription level and copy number of the CDKN2A/P16 gene using public pharmacogenomics datasets [30, 31]

Summary

Introduction

The ability to sustain uncontrolled cell proliferation is one of the hallmarks of cancer cells [1]. The normal process of cell division depends on the cell cycle, a series of highly regulated steps manipulated by a set of specific cyclins that act in association with cyclin-dependent kinases (CDKs) [2,3,4]. The CDK4/6 complex plays a key role in cell cycle progression via monophosphorylation of retinoblastoma protein (RB) and subsequently promotes G1-S phase transition [5, 6]. The clinical implementation of first-generation nonselective CDK inhibitors was originally hampered by the high toxicity and low efficacy of these agents [7, 8].

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Discussion

Conclusion